RetrogeneDB ID: retro_oind_32

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 6:8991280..8993056(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA022637
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA004342
• Aliases: None
• Description: None

Sequence

>retro_oind_32
ATGGCCGCTAGAAGCGAGCTTCTCCGGCCGGCATTTGGTGAAGCATCTCCTTCGCTAGGACGGTTTGTCATTAACCCTCA
CAGCTGCAGCTACAGGTGGTGGCACATGTTCCTGATCATGCTGGTGTTGTACTCGGCATGGGCATCGCCGTTCGAGCTGT
CCATGGAGAAGGCAGCCTCCATTGCTCTTGTTGTCACAGACCTGGTGGTCGATGTCTTCTTCGCCATTGACATTGCCTTA
TCCTTCTTCGTCGCATACCGTGACACCTCCACCGGCCTCCTCATAACTGACCGCAGGAAGATCACAATGAGGTACCTGAA
ACGGCCGTGTTTCGCTCTGGATGTGGCCTCGACGATTCCTTTACAAATAATCTACCAGCTTGTGACTGGCAAAAGACAAG
GACTGTGGGGGCTCCTCAATCTTCTCCGTCTTTGGCGACTACGGCGCGTCAGCAAGCTCTTTGCGAGGGTGGAGAAGGAC
ATCAGATTCAACTATTTGTGGACCAGGCTTATCAAGCTCCTTTGTGTGACACTGTTTGCGCTGCATTTTGCCGCTTGCAT
CTACCTGTGGATGGCATTCAACTACAAGATCAAGGAGCTTACATGGATAGGCAGCCAGATCCATAGCTTTGAGGACCGAA
GCGTGTGGTTTTGCTACACCTGTGCAGTGTACTGGTCCATCACCACGCTTGCCACGGTCGGCTACGGTGACCTACATGCC
ACCAACATTGGCGAGATGCTTTTCAGCATAGCCTTCATGCTTTTCAACATGGGCCTCACATCCTACATCATCGGCAACAT
CACCAACCTCGTTGTCCGTGAAACCTCCAACACCTTCAAGATGAGGGACATGGTGCAGCGGGTGTCGGAGTTCGGGAGAA
TGAACCGGCTGCCAGAGGCGATGAGGGAGCAGATGTTGGCCAGCGTGCAGCTCAGGTTCAGGACAGATGAGCAGCTGCAG
CAGGAGATGTTGTCAGAGCTGCCCAAGGCTGTGCGGTCGGGCGTCATGAAGCACATGTTCAAGAGTGCTATCGAGAGCTG
CTACCTATTCCAGGGAGTCTCCGACAGCCTCATTGTGCAGCTGGTCGCGGAGATGAAAGCAGAATTCTTTCCCCCCAAGG
CTAATGTTATCCTAGAGAATGAGACCTCGACGGACTGTTATATCATCATCTCTGGCGAAGTGGAGGCATTGACAACCCTT
GCAGATGGGACAGAGAAGCATGTGAAGAGAATAGGACCTCGGGGCATGGCAGGGGAAATCGGGGTGATGTTCAGCATTCC
GCAACCATTCACCATCCGGAGCAGGAGACTCACCCAGGTTGTCCGCATAAGCCATATCCATCTGCTTCAGGCTGTCCGGC
CTAACACCGCAGATGGGTACATCGTGTTCTCCAATTTTATTCAGTACCTTGAGTCTCTGAAGGTGCAAACAAAGGATGTG
GCTTTTGTCAGCGATCATCTTTGGAATGGAAACTCAATGGTTTTGGGAAGGGCAACCGAGGTTGCTGTAGATGAATCAAA
AGAGGCCGCTCACAAAATGTTACCATGCAAAGAACCCAAACGGGTTGTTATTCATGAGCAACTTCCCAACGCGACTAGCA
CAGCACTGCATCCTTCGCCGGGGAAGCTCGTCTTACTCCCAGATTCGATGCAAGAACTGATGAAACTTTCAGAAAAGAAA
TTTGGGAAGGCCGTGAGAGGGATCCTCACTGTGGAAGGAGCCGAGGTTGAGGACATTGAAGTGATAAGAGATGGCGATCA
CCTGTTATTTAGTTAG

Alignment

ORF - retro_oind_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.68 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASRSELLRPAFGEPSPSLGPFVVNPHTCSYRWWQKFLIVLVLYTAWASPFELAMEKSASAALAVTELVVD
          A.RSELLRPAFGE.SPSLG.FV.NPH.CSYRWW..FLI.LVLY.AWASPFEL.MEK.AS.AL.VT.LVVD
Retrocopy AARSELLRPAFGEASPSLGRFVINPHSCSYRWWHMFLIMLVLYSAWASPFELSMEKAASIALVVTDLVVD

Parental  AFFAVDIAVSFFVAYRDASTGLLVTDRKKIATRHLARPCLALDVASTIPLQMIYRIVSGKRQALYGFLNL
          .FFA.DIA.SFFVAYRD.STGLL.TDR.KI..R.L.RPC.ALDVASTIPLQ.IY..V.GKRQ.L.G.LNL
Retrocopy VFFAIDIALSFFVAYRDTSTGLLITDRRKITMRYLKRPCFALDVASTIPLQIIYQLVTGKRQGLWGLLNL

Parental  LRLWRLRRVSKLFARLEKDIRFSYLWTRLIKLLYVTLFAVHFASCIYLWMAFHHKAKELTWIGSQFHGFE
          LRLWRLRRVSKLFAR.EKDIRF.YLWTRLIKLL.VTLFA.HFA.CIYLWMAF..K.KELTWIGSQ.H.FE
Retrocopy LRLWRLRRVSKLFARVEKDIRFNYLWTRLIKLLCVTLFALHFAACIYLWMAFNYKIKELTWIGSQIHSFE

Parental  DRSVWFCYTCAVYWSITTLATVGYGDLHAANTGEMLFSIAFMLFNMGLTSYIIGNITNLVVHETTNTFKM
          DRSVWFCYTCAVYWSITTLATVGYGDLHA.N.GEMLFSIAFMLFNMGLTSYIIGNITNLVV.ET.NTFKM
Retrocopy DRSVWFCYTCAVYWSITTLATVGYGDLHATNIGEMLFSIAFMLFNMGLTSYIIGNITNLVVRETSNTFKM

Parental  RDMVQRTSVFGRTNRLPVAMREQMMESLQLRFRAEEQLQQEMLSELPKAVRSGIAQHMFRGAVQSCYLFQ
          RDMVQR.S.FGR.NRLP.AMREQM..S.QLRFR..EQLQQEMLSELPKAVRSG...HMF..A..SCYLFQ
Retrocopy RDMVQRVSEFGRMNRLPEAMREQMLASVQLRFRTDEQLQQEMLSELPKAVRSGVMKHMFKSAIESCYLFQ

Parental  GVSDKLVLPLVAEMKAESFPPKADIILENEASTDCYIIVSGEVEVLTTLEDGTEKQVMRIGPRGMAGEIG
          GVSD.L...LVAEMKAE.FPPKA..ILENE.STDCYII.SGEVE.LTTL.DGTEK.V.RIGPRGMAGEIG
Retrocopy GVSDSLIVQLVAEMKAEFFPPKANVILENETSTDCYIIISGEVEALTTLADGTEKHVKRIGPRGMAGEIG

Parental  VMFNIPQPFTIRSRKLTQLVRISHSHMVSTIRPNTADGVVVFSNFVLYLESLKVKAKETAFVRDHLRNGY
          VMF.IPQPFTIRSR.LTQ.VRISH.H.....RPNTADG..VFSNF..YLESLKV..K..AFV.DHL.NG.
Retrocopy VMFSIPQPFTIRSRRLTQVVRISHIHLLQAVRPNTADGYIVFSNFIQYLESLKVQTKDVAFVSDHLWNGN

Parental  STVLGSATMFDVDESKESAHKMLPCKEPKRVSIHEHLLNGTGTALNGSSGKLVILPDSMQDLMKLSEKKF
          S.VLG.AT...VDESKE.AHKMLPCKEPKRV.IHE.L.N.T.TAL..S.GKLV.LPDSMQ.LMKLSEKKF
Retrocopy SMVLGRATEVAVDESKEAAHKMLPCKEPKRVVIHEQLPNATSTALHPSPGKLVLLPDSMQELMKLSEKKF

Parental  GKAARGILTVGGAEVEDIEVIRDGDHLFFS
          GKA.RGILTV.GAEVEDIEVIRDGDHL.FS
Retrocopy GKAVRGILTVEGAEVEDIEVIRDGDHLLFS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_32 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32 ,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40,